Nickel in PDB 6n97: Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Amino(Dethia)-Coa

The structure of Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Amino(Dethia)-Coa, PDB code: 6n97 was solved by L.M.Stunkard, A.D.Dixon, T.J.Huth, J.R.Lohman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.961, 114.614, 192.338, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 17.9

The binding sites of Nickel atom in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Amino(Dethia)-Coa (pdb code 6n97). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Amino(Dethia)-Coa, PDB code: 6n97:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Amino(Dethia)-Coa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Amino(Dethia)-Coa within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:66.2 occ:1.00 NE2 B:HIS220 2.2 46.4 1.0 NE2 A:HIS220 2.2 37.8 1.0 NE2 C:HIS220 2.4 36.3 1.0 CE1 B:HIS220 3.0 41.0 1.0 CE1 C:HIS220 3.0 37.1 1.0 CE1 A:HIS220 3.1 41.6 1.0 CD2 A:HIS220 3.2 41.0 1.0 CD2 B:HIS220 3.2 42.3 1.0 O B:HOH621 3.3 56.2 1.0 CD2 C:HIS220 3.4 37.0 1.0 O A:HOH666 3.9 48.4 1.0 ND1 C:HIS220 4.0 39.4 1.0 ND1 B:HIS220 4.1 40.9 1.0 ND1 A:HIS220 4.2 40.0 1.0 CG C:HIS220 4.3 31.0 1.0 CG B:HIS220 4.3 34.5 1.0 CG A:HIS220 4.3 31.2 1.0 O C:HOH581 4.6 31.3 1.0 O C:HOH683 4.7 49.1 1.0 O B:HOH574 4.7 34.0 1.0 O C:HOH478 4.8 32.6 1.0 O A:HOH533 4.8 34.8 1.0 O B:HOH527 4.9 32.4 1.0

Nickel binding site 2 out of 2 in the Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Amino(Dethia)-Coa


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Methylmalonyl-Coa Decarboxylase in Complex with 2-Sulfonate-Propionyl- Amino(Dethia)-Coa within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni301 b:59.2 occ:1.00 NE2 F:HIS220 2.2 41.2 1.0 NE2 E:HIS220 2.3 40.1 1.0 CE1 D:HIS220 2.6 38.8 1.0 NE2 D:HIS220 2.8 38.1 1.0 CE1 F:HIS220 3.0 44.9 1.0 CE1 E:HIS220 3.0 38.4 1.0 CD2 F:HIS220 3.3 40.8 1.0 O F:HOH640 3.4 35.6 0.5 CD2 E:HIS220 3.4 40.4 1.0 ND1 D:HIS220 3.6 43.2 1.0 CD2 D:HIS220 4.0 37.6 1.0 ND1 F:HIS220 4.2 43.5 1.0 ND1 E:HIS220 4.2 36.4 1.0 CG F:HIS220 4.3 28.9 1.0 CG D:HIS220 4.4 30.3 1.0 CG E:HIS220 4.4 28.8 1.0 O F:HOH635 4.4 36.1 0.5 O D:HOH607 4.6 33.1 1.0 O E:HOH576 4.8 32.0 1.0 O E:HOH504 4.8 33.7 1.0 O D:HOH702 4.8 47.1 1.0 O D:HOH482 4.8 34.9 1.0 O F:HOH509 4.9 30.6 1.0 O F:HOH640 4.9 24.1 0.5 O F:HOH548 4.9 28.6 1.0

L.M.Stunkard, A.D.Dixon, T.J.Huth, J.R.Lohman. Sulfonate/Nitro Bearing Methylmalonyl-Thioester Isosteres Applied to Methylmalonyl-Coa Decarboxylase Structure-Function Studies. J. Am. Chem. Soc. V. 141 5121 2019.
ISSN: ESSN 1520-5126
PubMed: 30869886
DOI: 10.1021/JACS.9B00650